From patchwork Tue Oct 31 10:57:28 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 55724 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id C985327BBEA; Tue, 31 Oct 2023 11:00:28 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 5F37327BBE2 for ; Tue, 31 Oct 2023 11:00:28 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qxmTM-0006cW-EG; Tue, 31 Oct 2023 06:59:48 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qxmTB-0006T8-7G for guix-patches@gnu.org; Tue, 31 Oct 2023 06:59:38 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qxmT9-0003ZR-Sm for guix-patches@gnu.org; Tue, 31 Oct 2023 06:59:36 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qxmTh-000622-Hc; Tue, 31 Oct 2023 07:00:09 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#66843] [PATCH 10/11] gnu: Add r-coregx. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: rekado@elephly.net, guix-patches@gnu.org Resent-Date: Tue, 31 Oct 2023 11:00:09 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 66843 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <66843@debbugs.gnu.org> Cc: Ricardo Wurmus X-Debbugs-Original-Xcc: Ricardo Wurmus Received: via spool by 66843-submit@debbugs.gnu.org id=B66843.169875000623106 (code B ref 66843); Tue, 31 Oct 2023 11:00:09 +0000 Received: (at 66843) by debbugs.gnu.org; 31 Oct 2023 11:00:06 +0000 Received: from localhost ([127.0.0.1]:47561 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qxmTd-00060T-3A for submit@debbugs.gnu.org; Tue, 31 Oct 2023 07:00:05 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:43665) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qxmTC-0005x4-GJ for 66843@debbugs.gnu.org; Tue, 31 Oct 2023 06:59:39 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1698749938; x=1700564339; bh=+DOzaNpeQmNJKcUBYCqDRvlx52OjVCrdC6omV0Ixa2U=; b=YeMMdgd308Fj p+fv92aa0Ulrn/9UEtin+En+1my36dfCrz8jWv5TGe/EX12phAK7D+ezf2g/LZ+R KMBhYNmEHtFprlJH9l6nPDfosphjENEYSAGioNXBEoh9ijxW8PpQKjBMswfk8u9O 0issWkt19IJBLUFq66hDNyFrJi1KIFw= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id 9EE5516017D for <66843@debbugs.gnu.org>; Tue, 31 Oct 2023 11:58:58 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Tue, 31 Oct 2023 11:58:57 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Tue, 31 Oct 2023 11:57:28 +0100 Message-ID: X-Mailer: git-send-email 2.41.0 In-Reply-To: <4d5576bdd09911a6a51bbe87a1b905bd07ca0c4b.1698749849.git.madalinionel.patrascu@mdc-berlin.de> References: <4d5576bdd09911a6a51bbe87a1b905bd07ca0c4b.1698749849.git.madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27968.007 X-TM-AS-Result: No-10--14.023100-5.000000 X-TMASE-MatchedRID: n8dyCgqCzuv/R1NSMc2qCTiEPRj9j9rvwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v8XjfR3d0weRhItcoSAIccJFYR GbK7nAWgKsykCO9ZPU6fXwOj91l33yGl4XmOxPLZOG5AmSMA4voGIsNQKxyHbqshboLxjPXYs28 FPOedmEpST9wVeygStLmth8cTQ473Q3sOMB3Fk1OLzNWBegCW2wgn7iDBesS3CttcwYNipXxjOl t1Pi553v9BIZrOFM/0+e/ht+ujEJs00RHzmU/HJJhOIk2Jg6W8= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--14.023100-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27968.007 X-TM-SNTS-SMTP: D7315A99F6736E0E4F4095B8608D48859C8D6B9705054678853E808FAACEA8FC2000:F X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-coregx): New variable. Change-Id: Ib54ba3c7bebdcc90748d4e4b0b2ce63b7f0fc1b8 --- gnu/packages/bioconductor.scm | 46 +++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e2fd9c5016..091cf98b5c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4422,6 +4422,52 @@ (define-public r-cellid enrichment in single cell data.") (license license:gpl3))) +(define-public r-coregx + (package + (name "r-coregx") + (version "2.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "CoreGx" version)) + (sha256 + (base32 "09pv117g8sxhrij960mparrz1r9vx8s20gmpvn1h667kl1bc0jm9")))) + (properties `((upstream-name . "CoreGx"))) + (build-system r-build-system) + (propagated-inputs + (list r-bench + r-biobase + r-biocgenerics + r-biocparallel + r-bumpymatrix + r-checkmate + r-crayon + r-data-table + r-glue + r-lsa + r-matrixgenerics + r-multiassayexperiment + r-piano + r-rlang + r-s4vectors + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/CoreGx") + (synopsis + "Classes and functions to serve as the basis for other Gx packages") + (description + "This package provides a collection of functions and classes which serve as +the foundation for our lab's suite of R packages, such as PharmacoGx and RadioGx. +It was created to abstract shared functionality from other lab package releases +to increase ease of maintainability and reduce code repetition in current and +future Gx suite programs. Major features include a @code{CoreSet} class, from +which RadioSet and PharmacoSet are derived, along with get and set methods for +each respective slot. Additional functions related to fitting and plotting dose +response curves, quantifying statistical correlation and calculating +@acronym{AUC, area under the curve} or @acronym{SF, survival fraction} are +included.") + (license license:gpl3+))) + (define-public r-coverageview (package (name "r-coverageview")